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Rice (<i>Oryza sativa</i> L.) chalkiness greatly reduces the rice quality and the commercial value. In this study, <i>qWCR4</i>, a previously reported quantitative trait locus (QTL) of white-core rate (WCR), was confirmed by a BC₅F₂ segregation population and further fine mapped to a 35.26 kb region. In the <i>qWCR4</i> region, <i>LOC_Os04g50060</i> and <i>LOC_Os04g50070</i> showed significant differences in expression level in endosperm between two NILs, whereas four other genes had no expression. Starch granules in the central endosperm of chalky grains from NIL(J23B) with higher WCR exhibited a typically round and loosely packed morphology. NIL(J23B) with higher WCR accompanied a higher seed filling speed. Moreover, <i>qWCR4^J23B</i> (<i>qWCR4</i> allele in J23B) increased WCR, grain numbers per plant, seed setting rate, grain width, and thousand-grain weight, contributing to a superior yield per plant. All in all, our research results not only lay a foundation for map-based cloning of <i>qWCR4</i> but also provide new genetic resources for rice yield and quality breeding.